Re: Taxon Search

[David Marjanovic <david.marjanovic@gmx.at>]

> --- Ursprüngliche Nachricht ---
> Von: "Jaime A. Headden" <qilongia@yahoo.com>
> Datum: Fri, 9 Dec 2005 23:11:08 -0800 (PST)
>
> David Marjanovic (david.marjanovic@gmx.at) wrote:
>
> <It is quite interesting and makes several very good points, but I
> wouldn't quite call it "excellent".>
>
>   So it would need to be flawlessly perfect, or perhaps supportive
> of PhyloCode, to be "excellent"?

Why do you think so?

No, in order to be "excellent", it has to be more than "good". And I don't 
think it is. If you read the paper carefully, you will see that Sereno had 
not even understood the term "crown group", incorrectly claiming names of 
crown groups could have stem-based definitions, and had also failed to 
understand the (admittedly rather complicated) terms "stem-modified node-
based definition" and "apomorphy-modified node-based definitions", 
incorrectly claiming they were stem-based, while they are indeed node-
based (but their specifiers aren't mentioned explicitely, so this can be 
overlooked). He even claimed that apomorphy-based definitions were stem-
based, which they aren't -- he had fallen into a purely semantic trap of 
his own making. (In his preferred wording both types begin with "the most 
inclusive clade".) Then there are all the definitions which contain the 
phrase "and any extant species", a consequence of the misunderstanding of 
crown groups that is in the end nothing but misleading.

> <This starts with the (somewhat overblown) title -- there is no
> "phylogenetic taxonomy", only phylogenetic nomenclature.>
>
>   I beg to differ. Starting from a nomenclatural standpoint, we name
> things all the time, essentially assigning labels. This is all
> nomenclature means, the assignment for distinction of identifying terms. 

Yes, and this is _all_ that phylogenetic nomenclature does.

> Taxonomy, on the other hand, is related to phylogeny, and the
> nomenclature used by taxonomists either stems
> from or leads to phylogeny.

So by "taxonomy" you mean "the application of nomenclature"?

> While it is correct as Mike observes David to
> say, that taxonomy has relationships with ranks,

I haven't said that. I tried to say that taxonomy is the theory of 
classifying.

> it can name types of clades distinctly, such as nomenclature prefixing
> "Pan-" to total-content clade names

That's nomenclature, not taxonomy.

> Thus, taxonomy and nomenclature are both distinct, and the former need
> have nothing to do with Linnaean taxonomy.

I agree with that.

> <(The term "taxonomy" was invented as "the theory of classifications".>
>
>   The word evolution was originally used to imply that there is an ideal
> goal in progression of organisms, originally to define man's imperialism 
> above [...].

Actually it was first used for ontogeny, for embryogenesis. That's why the 
word means "unwrapping", "unrolling".

> Do we use the word in this way now?

No. "Taxonomy", however, is still used by some in its original sense.

> <People who apply phylogenetic nomenclature _do not classify_ -- they
> don't hack the Tree of Life apart and try to shoehorn the pieces into a
> set of boxes of predetermined sizes;>
>
>   I beg to differ: a crown taxon specifically
> requires the content to be living,

Yeah, and? ~:-| This isn't classifying.

(Not the content, BTW; just the internal specifiers.)

> and Sereno's (2005) criterion has appended this with an extinct
> external specifier,

overlooking (and denying) the fact that a clade with a stem-based 
definition cannot be a crown group.

> meaning that two living groups whom are each other's sister
> taxa cannot be crown taxa.

In his terminology they can be. In everyone else's they can't.

> Should be anchor "Pan-" to any total-content clade
> names we coin, and to ensure this relationship, rename all taxa used or
> definable as total-content clades to include "Pan-" as a prefix?

No, but that's a completely different topic... what's your point?

> Are these not somehow predeterminate?

Please explain what you mean.

> <Doesn't make any difference, except it allows somewhat more
> illustrative terminology.>
>
>   Linnaean systematics, aka, it's taxonomic system

...wasn't what I was talking about. I was talking about "tree-based" 
terminology ("the first organism... and all its descendants") and its 
difference to the "cladogram-based" terminology ("the most/least inclusive 
clade...") that Sereno prefers.

> an apomorphy-based clade, which is as Sereno points out, a potential
> type of stem-based clade.

No, it's not. Sereno worded apomorphy-based definitions as "the most 
inclusive clade diagnosed by apomorphy M", and because "the most inclusive 
clade" is also how he (correctly) words stem-based definitions, he thought 
the two were the same. But nothing would change if he worded apomorphy-
based definitions as "the _least_ inclusive clade diagnosed by M". In fact 
both adverbs are entirely redundant. Apomorphy-based definitions could 
just as well be worded as "_the_ clade diagnosed by M", because in reality 
there is only one such clade (even though our knowledge of the fossil 
record may not allow us to tell exactly which clade that is -- even if the 
phylogeny we assume is correct).

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